Table 2.
General Characteristics of Putative Horizontally Transferred Elements Found in the Genome of Xf Strain 9a5c
| Element | Integrase-like gene at the end | Next to tRNA | GC content variation | Codon bias | Overexpressed in PW medium | Relevant resident genes |
| GI1 XF0480-0536 | Transposases A and B | Asn-tRNA (5′) | Yes | Yes | Yes | 5 phage-related proteins 1 fimbrillin gene 1 virulence associated protein (VapE) |
| GI2 XF1718-1793 | Phage-related integrase | Gly-tRNA (5′) Thr-tRNA (3′) | Yes | Yes | Yes | 12 dehydrogenases/keto-reductases 1 fimbrillin gene 8 transcriptional regulators |
| GI3 XF0631-00641 | Phage-related integrase | Ser-tRNA (3′) | No | No | Yes | 1 DNA modification enzyme |
| GI4 XF1859-1885 | No | Lys-tRNA (5′) | Yes | Yes | No | 5 phage-related proteins from bacteriophage Pf3 |
| GI5 XF2108-2132 | Phage-related integrase | Cys-tRNA (5′) | Yes | Yes | Yes | 1 phage-related repressor protein 1 virulence-associated protein (VapE) |
| pGI1 XF0126-0140 | No | Ser-tRNA (5′) | No | Small | Yes | 2 copper resistance proteins 1 DNA polymerase III subunit |
| pGI2 XF0393-0437 | No | Gln-tRNA (5′) | Yes | Small | Partially at 3′ end | 4 toluene tolerance proteins 5 membrane transporters 3 recombination-associated nucleases |
| pGI3 XF855-0900 | No | Pro-tRNA (5′) | Yes | Yes | Partially at 3′ end | 7 membrane-related factors 1 stress-related factor (SurE) 1 hemagglutinin-like protein |
| pGI4 XF1119-1190 | No | Leu-tRNA (5′) Val-tRNA (3′) | Yes | Yes | No | Gyrase modulators (TedD/PmbA family) |
| pGI5 XF2156-2225 | No | Ser-tRNA (5′) | Yes | Yes | Partially at 3′ end | 2 DNA polymerase III subunits (from E. coli) 15 amino acid biosynthesis genes 1 hemagglutinin-like protein 1 aldehyde-resistance gene |
| pGI6 XF2715-2748 | No | tm-RNA (5′) | Yes | Yes | Yes | 10 restriction-modification proteins (in 2 operons) |
| PI1 XF2025-2087 | No | No | No | No | No | 15 conjugative genes (Tra, Trb operons) 4 efflux system proteins |
| XfP1 XF0678-0733 | Phage-related integrase | Val-tRNA (5′) | Yes | Small | Yes | 24 phage-related proteins, including replication, packaging and capside proteins 1 proteic killer and antidote (higA/higB) |
| XfP2 XF2478-2530 | Phage-related integrase | No | Yes | Yes | Yes | 24 phage-related proteins, including replication, packaging and capside proteins |
| XfP3 XF1564-1587 | No | No | Yes | Yes | Yes | Probably duplicated from XfP4 6 phage-related proteins |
| XfP4 XF1658-1711 | No | Arg-tRNA (3′) | Yes | Yes | No | 7 phage-related proteins |